In the fields of biochemistry and molecular biology, it is often desirable to be able to prepare stable and reproducible molecular constructs that may serve as templates or reagents in analytical schemes designed to detect the presence of organic and biochemical analytes.
In biomimetic nanotechnology one aims to construct complex, nano-scale supramolecular structures from modular units using a “bottom-up” approach inspired by biological systems. The pre-formed modular units are designed to undergo controlled and reversible self-assembly without external manipulation of individual molecules.1,2 This approach imitates the self-assembly of complex objects in biological systems, which produce large complex structures such as ribosomes and splicesomes from smaller modular structures by hierarchical folding and assembly.3 Moreover, such biological structures are dynamic, comprise moving parts and successfully bind and release dissociable factors during functional cycles.
The use of RNA as a medium for nanotechnology, has been called “RNA tectonics” and involves three steps:4,5 1) Conceptual, modular design at the level of 3D structure using computer modeling techniques, 2) realization of the 3D design as the requisite supporting secondary structure and 3) detailed design of uniquely folding sequence.2,6-8 Recent work in RNA nanotechnology has resulted in the design of artificial RNA units that assemble to form oriented filaments, closed complexes, and 2D arrays.4,9-11 The programmed assembly of RNA monomers (“tecto-RNAs”) requires specific tertiary interactions. These can be identified in atomic-resolution 3D structures or selected in vitro using SELEX methods.12 “Loop-receptor” interactions, which form between specific hairpin or internal loops and cognate receptor motifs, comprise an important type of tertiary motif that occurs recurrently in large biological RNA molecules. They are sufficiently weak to be readily reversible and occur in all large biological RNA structures.4,5,13 Loop-receptor interactions avoid plectonemic braiding of individual RNA stem-loops, which would entangle the interacting units and therefore require unfolding of secondary structure to form. Therefore they can be considered a simple form of paranemic binding motif. The diversity of artificial RNA self-assembling modules (“RNA tectons”) is limited by the availability and specificity of receptor-loop motifs. Accordingly, alternate binding motifs that allow for more programmability, while maintaining similar geometries, are desirable.
It is desirable to be able to develop RNA as a medium for (1) exploring principles of supramolecular self-assembly and (2) achieving nano-scale molecular design and construction of complex cooperative assemblies capable of realizing diverse functions and practical applications.
There is also a need for biomolecules that can be used as stable electrophoresis markers and electron microscopy markers.
There also remains a need for RNA constructs with increased stability, and those that may be readily and reliably applied in analytical methods and devices by using conformational strategies to bind, isolate and detect target biomolecules.
In this regard, it is desirable to be able to efficiently produce biochemicals that may be used to bind, isolate and detect target RNA sequences though Watson-Crick interactions, and to be able to readily determine when such interactions have taken place for analytical purposes.